Molly, is that you?
by drsherlockpotter
Summary: Set on the day of the Reichenbach Fall and the days and years after that. Molly leaves London the night after the fall, leaving sherlock and all her friends to question where she has gone. When they do finally see each other again, everything about her has changed. Sherlock, Molly, Moriarty, Lestrade, John, Donovan and Anderson all appear at least once. Molliarty.
1. Chapter 1

Molly, is that you?

Chapter 1

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**Hey Guys! So I decided it was a good idea (not really) to start writing a second fanfiction, even though I haven't finished the first one. But don't worry I am still writing the first one and both should be updated at least once a week.**

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**The Day Of The Reichenbach Fall**

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Molly Hooper was a smart woman, stuck between the side of the devil and that of the angels.

"You were wrong you know. You do count, you've always counted and I have always trusted you" the words flowed out of his mouth as she stood there speechless, of course this had been planned. Moriarty had told her, when Sherlock had no one else to turn to he would seek her help. So for that exact moment in time for him to ask her to help him fake his death, she wasn't surprised.

Wow faking two deaths in one day. How annoying she thought to herself as she grimaced the thought of the two men she loved dead. One shot in the head, laying on St Barts' roof and the other sprawled across the pavement outside one of the doors of the hospital.

Sherlock and Molly spent the next half an hour planning out what would happen, just like she had with Jim the night before. Taking a pint of Sherlock's blood, the same as yesterday with Jim and making up a drug to make Sherlock's pulse undetectable. Quickly enough everything was set out and packed away just in the time, when the lab doors opened to see John walk in.

A phone rang, John's. As he talked on the phone his facial expression changed to one of worry, he quickly hung up and turned to face Sherlock. "Mrs Hudson's been shot!" He said panicking, obviously waiting for Sherlock to say something. "Sherlock she's dying!" John said, still no answer. John rushed out of the doors again. Molly couldn't help but admire the short ex-army doctor, who always put others before himself. She used to be like that caring, Molly thought to herself, before she met Jim Moriarty.

Before she knew it Sherlock had sent a text to Moriarty and was walking out of the lab doors. Her and Jim's plans were in place and so were hers and Sherlock's, which she had already planned out with Jim and Sebastian. Her phone rang, picking it up to her ear to hear her fiancé's voice echoing through her head. "Me and Sherlock are about to start everything. Moran is on hand and you know what to do with Sherlock. After he wakes up, take him back to yours, once he falls asleep and if he doesn't, drug him. Once he is asleep change into the dress I have left in your wardrobe and text Sebastian. He will wait outside your apartment in one of the cars and pick you up."

"Ok yes I've got it." Molly replied.

"Love you darling" Jim said before hanging up and the phone went dead.

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Moriarty and Sherlock stood on the roof of St Barts, the wind whipping against their clothes and moving them in the wind, whilst staying alive played in the background. After a while of talking, Moriarty "shot" himself. Bursting the blood bag Molly had sorted out the day before with him and collapsed on the floor, playing dead. Sherlock turned around outraged that Moriarty had killed himself before he could call off the snipers aimed at John, Mrs Hudson and Lestrade. Picking up his phone he dialled John's mobile number, talking to him whilst letting a tear of two roll down his pale face before throwing his phone behind him letting it clatter on the floor upon impact, causing the it to smash. In one swift movement of his dark blue coat, he jumped off the building and landed in the laundry truck parked on the side of the road nearest the building, the soft cotton pillows and sheets preventing the impact of the fall from being too bad. Once he had landed, Sherlock quickly hopped off of the laundry bags to lay on the pavement. The last thing Sherlock remembered was Molly rushing over to him blood bag and needle in hand before pouring the blood over his head and inserting the needle into his arm.

Molly quickly scuttled back round the corner of the building to where she was previously watching the scene play out. The trick had worked with the cyclist, who had successfully knocked John to the ground and cycled off. She noticed John stumble as he got up from his position on the street and run over to the "dead" Sherlock, pushing through the crowd, checking his pulse and watching Sherlock being brought inside on a gurney they had just hoisted him onto.

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Molly received the phone call almost immediately. "Molly! You will never believe this, Sherlock Holmes is dead. Just jumped off of the roof, they're bringing him down as we speak." She heard her colleage say as the phone disengaged.

She moved over to the morgue doors to receive her next "patient", who moments later was rolled into her morgue by several paramedics. Signing the forms, the paramedics gave her an acknowledging nod before they left her and the new "corpse" alone in the cold, large morgue in the depths of the hospital.

Collecting the spare clothes in the corner of the room, she had left there earlier, Molly walked over to the table where Sherlock's bloody body laid and opened the body bad. Whilst waiting for Sherlock to wake up she sorted out the rest of the paper work her letter of resignation. She put her engagement ring back on for a while seeing as Sherlock was still unconscious and no one else was in the morgue. Hearing a groan, she slipped the ring off and walked over to the now conscious Sherlock. She passed him the clothes and turned around so he could put them on.

"We should leave now" Sherlock said as he walked over to Molly. "Yes ok. Just let me get my things" Molly replied. She picked up all her things and both Molly and Sherlock in disguise, left through the back door to the hospital, hailing a taxi as they walked towards the road.

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They both exited the taxi and walked towards Molly's flat. Placing the key in the lock, she turned it to reveal the interior in her medium sized flat. "Make yourself at home" She told Sherlock as he walked in behind her. He walked over to the sofa and sat down, making his hands into a steeple position position and resting them under his chin as he lay upon the whole length of the sofa.

"Right well I'm going to go get in the shower and changed out of my work clothes. Then I'll make some dinner, which should be ready by 6:30pm" Molly said as she made her way to her bedroom.

"Yes ok" Came Sherlock's response as he waved a hand at her.

Molly made her way out of her bedroom, now fully dressed in casual clothes and walked over to the kitchen. Sherlock was now sitting upright as he yelled at the TV, which was now playing Jeremy Kyle. "Keep it down will you" Molly said to Sherlock as his yelling got louder. "Fine yes"

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Sherlock got up from his spot on the sofa and walked into the kitchen, taking in the beautiful aroma around him. Molly stood by the stove, serving the contents of the frying pan into the two bowls. "Sherlock foods ready" She called before turning around to be face to face with the world's only consulting detective. "Smells lovely" he said. "Is that a compliment, Sherlock?" Molly replied. "I suppose so although it was also a statement" "That's as modest as you get isn't it?" "Yes" He replied before grabbing a bowl of the spaghetti Bolognese and sitting down at the dining table. Molly grabbed her bowl and joined him.

Both Molly and Sherlock sat in comfortable silence while eating, occasionally making small talk. Molly was the first to stand grabbing the bowls she walked over to the sink and started to wash up. "Do you want a coffee?" She asked him. "Yes" He replied as he walked back into the living room.

Molly got two mugs out of the cupboard and filled them up with coffee before pulling out the tablet capsule and emptying the contents into Sherlock's coffee. Stirring it in and making sure it had dissolved, Molly picked up the mugs of coffee and walked into the living room. She walked through the door and handed Sherlock his coffee, making sure she gave him the right one. Wouldn't want that happening, she thought to herself. Before walking over to her armchair to watch TV with Sherlock, whilst sipping her hot coffee.

Ten minutes later, Molly looked up from her book after hearing a loud thud on the carpet. Sherlock was slumped across the floor along with his coffee mug. "Good it worked" Molly said to herself. She walked into her bedroom and pulled out the dress Jim had put in her wardrobe and started to put it on. Walking out of her bedroom she put her ring back on the picked up a notepad, pen and the flat key. Placing all three objects on the table, Molly began to write a letter before sending a text to Sebastian.

**I'm ready, come and get me when you're ready. I've drugged Sherlock . – MH**

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Sebastian Moran parked the black Bentley with tinted windows outside Molly's flat. Picking up his phone he sent a text.

**Outside now, black Bentley. – SM**

Two minutes later Molly opened the front passenger door to the car and got in. Sebastian and Molly shared a quick conversation before the car drove off in the darkness of the night.

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Sherlock woke up to find himself laying on the floor to Molly's flat. Getting up, memories started to reappear in his head. Drinking the coffee, starting to feel limp, falling to the floor then seeing and hearing Molly kneel next to him and whisper in his ear "I'm so sorry Sherlock, maybe we will meet again in the future" Before he fell asleep. Standing up and walking towards the kitchen he noticed a letter and a key on the dining table. Sherlock picked up the letter and key and started to read the letter.

_Sherlock,_

_My time spent with you and the others has been absolutely amazing. Even when you said hurtful things you were still there for everyone in your own special way. I hope you succeed in taking down Moriarty's network, so you can return to the people closest to you. I feel it necessary to say sorry for drugging you but I didn't want you to follow me or see me go. Feel free to stay here as often as you want with the key I have left you but let it be known that I will not return, at least not anytime soon and I should be completely undetectable. I hope we meet again in a few years of decades, but until then goodbye Sherlock Holmes._

_Molly x_

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**I hope you have enjoyed reading this so far. Please feel free to write comments. Every chapter of this fanfiction is going to be set 2 days after reichenbach, 1 year after and so on until I get to the main bit in the last few chapters. So it's sort of leading up to what happens in the last few chapters.**

**Lucy x**


	2. Chapter 2

Molly, is that you?

Chapter 2

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**Hey Guys! Here's chapter 2 hope you enjoy and please feel free to write some reviews and comments after reading.**

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**Two days after the Reichenbach Fall**

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Molly walked down the isle of the church, music all around her as she walked in the beautiful white dress that clung to her body. The dress was lace and fitted at the top with a sweetheart bust and flowed out slightly from the waist downwards. She was holding a bouquet of red roses and had another slotted in hair among the flowing curls of her hair.

The ceremony was only small with only Molly, Jim, Sebastian and a few of Jim's and Molly's people. Molly continued to walk to the end of the isle until she was face to face with Jim. The priest asked them to say their vows: "Do you James Moriarty take Margret Hooper to be your lawfully wedded wife?" "I do" Jim replied. "And do you Margret Hooper take James Moriarty to be your lawfully wedded husband?" "I do" Molly replied. "Then I now pronounce you Mr and Mrs Moriarty. You may now kiss the bride."

They walked out of the picturesque church and had a photographer take some pictures outside the church and in front of the wild flowers. Waving to Moran and the others they drove off in the black car, heading towards the airport where their private jet would take them to America for their honeymoon. "I've arranged for you to do some recruiting while we're in America, since you don't have people over there. When we get back you can expand further." Jim said to Molly as they neared the airport. "Yeah, being the only consulting spy, I'm going to need lots more people to boss around. Soon the Moriarty Empire will be the biggest and greatest it has already been." Molly replied as Jim brought her closer to him, pecking Molly on the lips.

Before long they reached the airport, Jim got out of the car first and walked over to the other side of the car to help Molly out. The interior of the jet was silver and black, two long sofas lined most of the length of the plane and a coffee table rested in the middle of them.

"You should go get changed darling" Jim told Molly, seeing as she was still in her wedding dress. "Fine, but I just remembered I didn't post my letter of resignation to Mike Stamford" Molly replied. "Oh yes, I will get Seb to do that" "No don't, we could have a lot of fun with this. Tell him to get some of my blood, leave it around the flat, turn the furniture over and make the door look as if someone had broken in. Someone will see, phone the police and assume I'm dead." "I like how you think, I definitely married the most cunning woman in the world" He replied pulling Molly into his arms before she turned away and walked into another room of the jet to get changed.

When Molly returned, she was wearing a red knee length Armani dress and tall black heels. "I've called Seb, he's going to set up your flat just as you want it. Hopefully someone will notice by the end of the week, we have surveillance set up, so we know what is happening." "Good" Molly replied as she walked over to the sofa Jim was sitting on, picking up a glass of champagne on the way before sitting down. They spent the next few hours kissing and planning out what they were going to do while they were in America.

The jet descended onto the tarmac of the plane's runway, the tyres squeaking upon impact. The door to the plane opened after it came to a stop and Molly and Jim walked down the steps and into the car that was parked next to it.

The car drove for about an hour before parking up outside a mansion complete with pool. "So this is our American house" Jim told Molly. "It's lovely" Molly replied as both of them got out of the car and walked towards the house. The staff greeted them as both Molly and Jim walked into the house. Some of the staff rushed out of the house and towards the car, picking up their luggage and carrying it inside.

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The walls were either covered with books or paintings which gave the insides of the modern house a bit more of a classic feel. There were thirteen bedrooms, three living rooms and pretty much every corridor was a library. Molly hadn't been able to go to America for business before, since it would probably blow her cover. But now she was here for her honeymoon and business 'double whammy' she thought to herself.

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**A week and a half after the Reichenbach fall**

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Mike Stamford walked into the Morgue again. Molly had not turned up for her shift in a week and a half. 'Well she did just go through losing the man she loved' He thought to himself. 'I don't want to disturb John, god that man's distraught. Maybe Greg, yes he likes her and probably wouldn't mind going to her house and checking on her.' Mike picked up his phone and started to dial Greg's mobile number.

**"Greg"**

**"Mike, how can I help you?"**

**"I was just wondering, have you seen Molly in the last week and a half?"**

**"No why?"**

**"It's just she hasn't been showing up for her shifts and I can't reach her by phone. I was wondering if you could check in on her to make sure she is ok."**

**"Yes ok, that doesn't seem like her, even after what happened she should've said at least something to you"**

**"Thank you. Sorry I asked this from you, it's just I thought it may be easier if you talk to her instead of me."**

**"Sure Mike I'll go now"**

**"Thanks Greg"**

The phone line went dead and Mike went to finish his paperwork.

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Greg hung up the phone and made his way out of his flat and towards the road to hail a cab. He had finally left his wife and was living in a flat near Baker Street. A cab pulled up to the curb and he climbed in.

After about five minutes the cab pulled up outside Molly's building and Greg hopped out. He walked into the building and up the stairs until he reached the top floor, where Molly's flat is situated. Upon seeing Molly's door Greg ran into the flat. The door was slightly open, blood was smeared on it and there was scratch marks all the way down.

Inside the flat all the furniture was upturned and blood was soaked into the carpet and dripping down the walls. "MOLLY! NO, NO, NO, NO, NO!" Greg yelled. He pulled out his phone and called Sally Donovan.

The team from New Scotland Yard arrived half an hour later. Greg sat on the floor crying when Sally walked in, she pulled Greg up and into a warm embrace "All of my friends are leaving me one by one" he told Sally as she led them into the hallway, so forensics could do their job. "It's ok Greg, we'll find her." Sally told him reassuringly.

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Greg walked the corridors of St Barts, upon reaching the door of Mike Stamford's office he knocked on the door. "Come in" Stamford told him. "Mike, I need to talk to you about Molly" "Oh yes, how is she? Do you know when she's going to be back at work?" Mike started rambling. "Mike when I got to Molly's there was blood everywhere and no sign of her" Greg told him sitting down in the chair opposite Mike. "Oh god, I should've checked in with her last week after she didn't show up!" Mike told him. "It's not your fault, I didn't even think to check in with her before you called me earlier" Greg said putting his head in his hands.

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John sat in his armchair when Greg, Mike and Sally walked up the stairs and knocked on the door. "Come in" John said, almost in a whisper. He looked awful and smelt like alcohol even more than Greg. All three of them walked into the cluttered room frowning upon the sight of the frail form that was John Watson. "What do you want?" He managed to say. "It's about Molly, when was the last time you saw her?" Sally asked. "You know, when it was why?" John asked. Greg handed the pictures to John, who took them with caution. "This was her flat this morning" Mike told him. "What happened?" John asked flicking through the pictures of Molly's bloody, upturned flat. "We're not sure, the Yard is starting a full investigation into it" Sally told him.

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"Jim dear it's worked, they've found everything we had Seb plant in my flat." Molly told James as she sat in front of the computer screen, looking at the surveillance camera footage. "Good, good. They'll either assume you're dead or you've been kidnapped." Jim replied. "Hm… can't have them suspecting anything. I'll contact Mycroft and tell him to close the case in a week or two, seeing as they won't find anything." Molly said before walking over to join him in the pool.

**Thank you for reading. I will update within the next. Lucy x**


	3. Chapter 3

Molly, is that you?

Chapter 3

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**Hey Guys! Sorry it's been ages since I've updated, but I've been busy with school. Just as a quick note, I got a few comments asking me questions about the past two chapters, so just to clear a few things up:**

**1) Molly is not on Moriarty's side, she is on no ones side. They are just married and do not side, even though they love each other.**

**2) Molly, Sherlock and Jim are all the same. When Sherlock admitted that him and Jim were the same, it confirmed that all three are the same.**

**3) Sherlock does not know where Molly is and is confused about what happened between them.**

**4) Sebastian, Moriarty's right hand man is refered to as Sebastian Moran, although this is just a alliance for his real name which is in fact Sebastian Hooper, who is married to Irene Adler (now refered to as Irene Hooper) they also have a daughter named Isabelle (Who will not appear until later chapters, along with her parents).**

**Anyway this chapter should clear up one or two more questions people may have. Enjoy :) - Lucy x**

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**Two years before the Reichenbach fall - Molly**

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Molly walked into the Diogenes club in the heart of London. Mycroft had called her earlier, saying there was someone he wanted her to meet. Walking into the only room in the whole building you can speak in, she was met by the eyes a man she had never met before.

"Molly…" The elder Holmes greeted her.

"Mycroft, good to see you" Molly replied.

"Good to see you too. As I have already told you, there is someone I want you to meet." Mycroft told her, gesturing to the man sitting on the other side of his desk.

"James Moriarty, Consulting Criminal" Jim said standing up and holding up his hand. Molly took it. James met her hand with his before bringing it toward his lips and kissing it.

"Molly Hooper, Consulting Spy" Molly told him before sitting down in the chair next to his.

"Now we've got introduced. We can get down to business; I need both of you to go undercover in the Maldives tomorrow for a case, since we don't want Sherlock or any of your other friends knowing about your other profession, I would like you to go together." Mycroft said.

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**A year before the Reichenbach fall - Molly**

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Jim sat on the sofa in his flat when Molly opened the front door and walked in. "You know you're starting this whole game with Sherlock, just make sure neither of you get too hurt of even killed. I don't know what I would do without either of you. Remember that the only thing that we want to achieve from this is being able to move away and focus on our real jobs and making sure that Sherlock doesn't find out who I am."

"Yes dear I know. Plus considering the fact we are all the same, you, me and Sherlock. We need each other we are all the same; apart from the fact you're a girl." Jim replied

"Obviously" Was Molly's only reply.

"Dinner?" Jim asked.

"No I have an assassination to stage so, only came back to change. Maybe tomorrow" Molly said as she walked into the bedroom to change into something more fitting for her current job. Picking up her hand gun, a few minutes later she walked back into the living room wearing a dark blue, floor length ball gown.

"You look devious" Jim said as Molly walked towards the front door.

"Thank you darling" Molly answered flashing a smile in his direction before she stalked out of the front door in her glamorous outfit.

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**Two days after the Reichenbach fall - Sherlock**

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Sherlock rose from his seat on the sofa where he had been sitting for 24 hours previously. He still didn't understand where Molly had gone and what her intentions were. The only things that had changed in her flat from before he was drugged were the letter and key, which neither gave any indication to either question.

Picking up his new phone Sherlock started to dial Mycroft's number.

"Ah brother dear, I was wondering when you would call. You haven't sent for the car to take you to the airport yet." Mycroft's voice broke through the silence bitterly.

"Yes well I've had a few things on my mind Mycroft. Can you send me the security footage from the other night, outside Molly's flat please?"

"That will not be possible there is none all the cameras went dead, when I was trying to keep an eye on you, and was that a 'please' you included?"

"Yes it was, can you send the car now Mycroft. I have decided there is no dwelling on the past. I need to forget what happened with Molly that can wait until after I've taken down Moriarty's network." Sherlock finalised before hanging up the phone.

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**One year after the Reichenbach Fall - Molly**

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"WHERE THE HELL IS HE?!" Molly yelled as another contraction hit. "He's on his way Boss" Jonathan Patricks answered.

They were both currently in a private hospital in Dubai. Molly was now pacing up and down the length of the room while Jonathan steadied her. "He should be here in about ten minutes with your brother. Mycroft should be here in five minutes, but your sister and Irene are stuck in London, so they can't come." He told her.

**Five minutes later**

Mycroft Holmes drifted discreetly into the room, wearing a three piece suit. "Well Molly" He let out a sigh "You look lovely as per usual" he finished. The only he got as acknowledgement was Molly staring daggers at him. If looks could kill Mycroft Holmes would very well be dead at this point in time. "Don't give me that Mycroft, I look as if I've swallowed a basketball" Molly exclaimed looking down at the large bump which was currently her stomach. "How long until they reckon you will be ready to push?" Mycroft asked, breaking the awkward silence that had filled the room, looking at the heavily pregnant Molly. "About ten minutes ago but I refused until Jim gets here" She replied walking back over to the bed to sit down, escorted by Jonathan.

Jim Moriarty finally walked through the door to his Wife's hospital room closely followed by Sebastian Hooper. "HOW BLOODY LONG DOES IT TAKE TWO MEN TO GET TO A HOSPITAL!?" Molly yelled at both men as they tried to avoid being at the other end of Molly's wrath. "Considering I was in Africa, you didn't tell me you were flying to Dubai! Seriously what are you doing here? You knew you were due any day now." Jim said to her. "Yes I know that, but I had business to attend to." Molly replied defensively. "What could possibly so important?" "This business doesn't wait for anyone, you know that better than anyone Jim!" she yelled back as a flood of doctors and midwives filled into the big room.

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**One and a half years after the Reichenbach fall – Sherlock**

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The sky was getting darker as the mysterious man walked into the abandoned house. It was the perfect place to set up base for the night. In only two hours three major members of Moriarty's network would walk into the building opposite for a meeting.

He unloaded the gun from the case he was carrying and placed it beside him. His signature coat and scarf were gone and replaced by a leather jacket. His black curly hair was now shorter and there was no sign of a freshly pressed shirt or trousers to be seen.

Sitting in the darkness with the gun placed on his lap, he waited. Before long the lights in the house next door turned on and three silhouettes appeared behind the window he was facing. Within minutes Sherlock fired three gunshots in rapid succession. Three discrete thuds could be heard in the distance as the lifeless bodies of the men fell to the floor.

"Half way there" He whispered into the darkness as he gathered up the gun and case and made his way back towards the car Mycroft had leased him for the duration of his stay in Hawaii.

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**Three years after the Reichenbach fall/the return – Molly**

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"Boss, Mycroft has informed us that Sherlock Holmes has 'finished' dismantling your husband's network and plans to return to London and 221B Baker St tomorrow morning." Patricks said as he entered the large library.

"Good, I can sense he has missed them and wants to return. I will not stop him, for now our game is over." Molly replied getting up and walking towards the window of the lone castle, settled upon the large, private island herself and Jim owned.

"Very well, also your sister Tanya called while you were out. John and Mary have set a date for their wedding and she has told them you her 'friend' Beth Williams can make them a cake. They would love 'you' to and have invited 'you' to the wedding as well."

"I see, I'm looking forward to it" She said her lips curling up into a smile. Picking up the gun on the table next to her, Molly turned around and walked towards the door, before looking back at the slim, red haired man. "Anyway I've got some business to do. Need to see a man about some missile plans." Molly finished as she walked out of the door in a slim, jet black cat suit.

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**Three years after the Reichenbach fall/the return – Sherlock**

* * *

He knew which stairs creaked when stepped on, which direction the flat faced and what Mrs Hudson was making for dinner that night, but nothing could prepare him for what lay beyond the small wooden door at the top of the stairs.

He still had a key, so let himself in. John Watson sat on his armchair in the corner of the room '_just like old times' _Sherlock thought to himself as John lifted his head to be greeted by the sight of his 'dead' flatmate and best friend. "Sh… Sher… Sherlock?" The man stuttered. "John" Sherlock replied.

"You… you're… supposed to be dead!" The short man's temper rising as he leapt out of his chair and walked faster than a man should over to Sherlock. "John, I can explain" Sherlock started as John's fist connected with his left cheek and he collapsed on the floor, blacking out completely.

After John realised what he had done, he started pacing the flat, questions forming inside his brain. Mrs Hudson and Greg chose that exact moment to walk into the flat. Witnessing the sight of Sherlock on the floor, they both looked at him questioningly. "Is that Sherlock?" Greg asked making his way over to the limp and unconscious body of his friend. "Yes" Was John's only reply as he slumped back into his chair, letting the previously unshed tears stream down his face.

* * *

When he finally arose into consciousness, all three of the other people in the flat were drinking cups of tea and staring at him inventively. "Well it's nice to see all of you" Sherlock said, picking himself up off of the floor and into 'his' chair.

"You better have a good reason for this Sherlock, or God forbid I might do something I might regret!" John started, placing his half drunken tea back onto the coffee table.

"I suppose I should tell you outright before you punch me again then. Moriarty had snipers set on all three of you and if I didn't jump he would've killed you. So I faked my death and spent the last three years tracking down his network and clearing my name…" He trailed on.

* * *

**One month after the return**

* * *

Molly walked into the room carrying the most beautiful cake ever. Blue swirls and patterns covered the white icing layer and bride and groom figurines resembling the features of both John and Mary stood proudly at the top. The room gave off the feeling of warmth and comfort but these were things she found unsettling and instead made her uncomfortable. Warm oak tables and chairs lined the outskirts and centre of the room. The room also backed onto others, to the left a ball room and to the right a bar.

She still had another five minutes to spare before the wedding party got there, so she went to order a drink at the bar. Picking up her phone, Molly began to compose a text.

**Thank you for the cake, it looks wonderful. Take the rest of the day off. M**

* * *

The wedding party filled into the room rapidly, the once undisturbed place, now filled with laughter, applause and tears of happiness. No one would be able to spot her in her disguise, the long blonde haired wig bounced with waves and cascaded down her shoulders and her brown eyes were replaced by bright blue contacts. That paired with a pretty dress and heels, made her look nothing like her normal self, or at least the one they knew.

Out of the corner of her eye, Molly could see Greg and Tanya dancing. '_They make such a great couple'_ she thought to herself. Her sister deserved a good man and Greg Lestrade definitely fit the description.

The next person she spotted was Sherlock himself, making his way towards the bar, paying no attention to her what so ever. He stood next to her and ordered the drink he desired, sitting down with a thud on the stool which nestled gently under the bar's surface.

Without thinking Molly pulled out the large envelope she was hiding in her bag and slid it in front of his eyes. The package almost screaming 'open me' Hesitantly Sherlock opened it warily, pulling out two more envelopes reading 'Birthdays' and 'Christmas'.

"Who are you and what is this supposed to be?" Sherlock questioned looking up at her. "You really don't remember me Sherlock? I'm hurt. They're cards addressed to you, John, Lestrade and Mrs Hudson for both their Birthdays and Christmases. Although it's completely up to you to tell them I'm not really dead." Molly replied, picking up her scotch and taking a sip, the liquid bringing warmth to her insides as it trickled down her throat.

"Molly?" He questioned. She nodded, confirming his question. "Let's leave questions until another time shall we Sherlock, as you can see we're both quite busy." Molly told him rising from her stool and walking towards the door. "Till the next time" and with that she disappeared into the night, not to be seen anytime soon.

He sat there for nearly an hour trying to make sense of what had happened until finally Mrs Hudson approached him, raising his mind from the thoughts and started to pull him towards the inviting dance floor, crowded with people.

* * *

**Two months after the return – Molly**

* * *

Steam rose up from the many coffee cups and plates of hot food which filled many tables in the restaurant. In the corner sat Tanya Hooper and Greg Lestrade, although at this point in time Tanya went with the last name of Brown.

Molly picked up the two champagne glasses, one of which contained an engagement ring as well as the bubbly liquid and made her way towards their table. Her sister would recognise her and wonder why she was there, but Greg wouldn't see through the disguise, mainly because he thought Molly was dead. Placing the glasses down on the table, Molly winked at her sister before walking away.

Looking down at the glass of champagne Tanya noticed the beautiful gold band with a single diamond placed in the centre. Taking it out of the glass she stopped to admire the way the diamond sparkled in the lights of the restaurant. Before Tanya could say anything, Greg took the ring out of her hand and got down on one knee, the whole restaurant turning to look at them.

"Tanya Brown, will you do the honours of marrying me?" Greg asked leaving her speechless, now Tanya understood why her sister was here at least. "Yes, of course!" Tanya exclaimed, tears rolling down her cheek.

Molly watched from afar smiling as her sister and future brother in-law got engaged. Setting down her waitressing apron and notebook, she left through the restaurant door.

* * *

**Eight months after the return – Molly**

* * *

Assassins climbed the walls and attempted to infiltrate the security. Helicopters and agents circled the perimeter, trying to find a way to enter the massive mansion.

Screams could be heard from within the house, even though it was in lockdown. In the heart of the mansion, Molly sat sweat dripping down her frail face and forming a small puddle on the floor.

"We need to do something soon" The doctor told Jim, Tanya, Seb and Jonathan. "She's getting in a bad way and there is no way of getting her out of the house" He finished. "What do you suggest we do?" Tanya asked. "Well in all fairness we need to perform an emergency C-section, but for that we need somewhere to do it safely, without the worry of someone putting a bullet in her brain or the baby's." He replied.

"We could move her downstairs into base. There is a load of medical supplies there, you could use." Seb offered. "Yes, that'll have to do, seeing as there is no other option. Although we'll have to move fast, seeing as Molly's starting to look really bad." The doctor replied, looking at Molly's pail and heavily pregnant form.

* * *

Heavy, hot air filled the atmosphere of the smallish room. Seb and Jonathan had left to fend off some of the assassins whom were now roaming part of the house, their only objective to kill Molly and her unborn child.

The doctor made a clean cut with a scalpel into the centre of Molly's stomach, dragging it the width of her body, before pulling it out. They hadn't sedated her as there was no medication available, so she clung onto her younger sister's hand and screamed at Jim. "Why the hell did I want another child!?" She said in hysterics. "I'M GIVING BIRTH TO THE DEVIL'S CHILD BLOODY 2.0!" She yelled, laughing again, using up more of the air in the already stuffy room.

Within minutes the doctor had pulled out a tiny baby from her womb. Tiny arms and legs flailing everywhere as he was placed in Molly's arms. "Oh my God, he's so cute!" Tanya exclaimed. "Now I've got a niece and a nephew." She continued laughing, reaching down and letting the baby's tiny fingers and hands capture one of her fingers and grip it tightly, as if the world depended on it.

"I quite like the name Thomas, it's quite sweet and innocent, no one would suspect him" Jim said pointedly at Molly, reaching down to kiss her forehead and admire the tiny small child in her arms, which he could wholeheartedly call his.

"Hmm… I like that name" Molly replied in recognition. Thomas looked more like his mother than his father. He had Molly's nose, but James' eyes. Unlike Ella, who had her mother's eyes and hair, where as she had her father's nose and facial structure.

Tanya stood there for a few minutes admiring the scene in front of her, until Seb walked back into the room, carrying Ella and placing her in Jim's arms. They looked like a proper family, a husband, wife and two children. But in reality they were the two geniuses, whom the whole world of countries and governments bowed down to and their children.

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**Thanks for reading! Will post up the next chapter as soon as I can and it will contain all the characters reuniting once again. - Lucy x**


	4. Chapter 4

Molly, is that you?

Chapter 4

**Hey Guys! Chapter 4, wow wasn't sure how I was going to lay it out, so it might not be brilliant but oh well. Hope you like it anyway - Lucy x**

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**One year after the return – Sherlock**

* * *

Greg, Anderson, Donovan, John and Sherlock were sat around a large table in one of the conference rooms at Scotland Yard.

"So" Greg started. "Target is Michael Justicia. He should be attending a social gathering at a mansion on the outskirts of London tonight. The owners of the house are apparently extremely intelligent and important to a lot of countries; their names are Mr and Mrs Abbott, although that is just an alias. However we do not know their real names, so extra care will need to be taken. Anyway getting on, we will be going undercover without disguises, only alias' and back stories. Anderson, Donovan, you will be posing as Robert and Alice Silverton. Sherlock, you will be Fredrick Winters and John will be your brother, Cory Winters. I myself will be Simon Walters."

"We should make a base, so that we can exchange information throughout the night, maybe in a drawing room or something" Sally suggested.

"Yes, that should work, as long as we are discreet about it and only meet every few hours" Greg replied eagerly, everyone standing and going to get changed, ready to leave in the next hour.

* * *

The summer night's breeze hit their clothes as Greg, Sherlock, John, Anderson and Donovan walked across the mansions drive and towards the large front door. It was formal attire so Sherlock, John, Greg and Anderson were wearing suits, whereas Sally was wearing a floor length green ball gown, which went with her complexion perfectly.

The main hall which branched off from the front door was covered with beautiful furniture, old paintings and pretty antiques.

"We should meet up in the drawing room in thirty minutes" Sherlock said as he moved away from the group and into one of the adjoining rooms, trying to figure out the mystery behind the owners of the house as well as finding out more about this Michael person, leaving the others to their own devices.

* * *

They were getting closer as Molly ran around the corners of the mansion. Michael had already killed her parents and she was determined he would never get his hand on the rest of her family. Every one of her England team were involved, whether they were doing field work or manning the computers and the rest of base.

She rounded the corner to the corridor which led to the drawing room and picked up her pace, running to the door as if it was the only thing that could keep her alive. Grabbing onto the door handle she opened the door and thrust herself inside, grabbing onto the end of the table for support as she felt her legs start to buckle. Finally looking up Molly realised she wasn't alone and was greeted by the site of Sherlock, John, Greg Lestrade, Sally Donovan and Anderson, who looked at her in disbelief.

She was about to say something when a gunshot rung out, piercing the window and hitting her side. This time her legs gave way and she fell to the floor, grabbing the gun which fell with her, Molly picked it up and with one quick shot fired at the gunman standing on the grass near the window, killing him instantly.

"Molly?" Greg questioned as blood started to trickle down her red dress and onto the antique carpet. "Yep, so you didn't tell them then Sherlock? I'm almost disappointed." A small smile creeping onto her lips as she looked up towards Sherlock.

"What are you doing here Molly?" Sherlock questioned.

"Got a bit bored, thought it would be fun running for my life" Molly replied laughing weakly, the blood loss starting to get to her. "John would you be a dear and patch this up quickly. Need to be at my best for Michael."

"But you're supposed to be dead Molly, you scared us half to death. Michael? What do you mean be at your best for him and for crying out loud did you just kill a man?!" John said taking a step closer, Donovan and Anderson still staying in exactly the same place they were sitting when Molly had rushed into the room.

"Yes I know John, but if you don't do anything now I will probably actually die this time. Yes I know him and yes I did just kill a man. Problem?" Molly pointed out. "There's a first aid kit in the cabinet over there" She said pointing towards a cabinet, which was situated on the right hand side of the room and had the world atlas painted onto it.

"How do you know that?" Sally questioned. "I have my ways" Molly replied swiftly as John walked back towards the group, now carrying the first aid kit.

"You're going to have to take your dress off Molly and also do some explaining" John pointed out coming to sit on the chair next to her.

"Fine whatever" Molly replied standing up, undoing the zip to her dress and letting it fall. Stepping out of the puddle of clothing, she went and sat back down on the chair again. Picking up John's phone discretely, not bothering to look at the expressions of the others faces.

"Um Molly, what are those stitches for?" Greg asked looking at the stitches that lined the width of her stomach. "John, Sherlock. Any guesses or contributions?" Molly asked looking in Sherlock's direction.

Sherlock gulped "They're C-section scars, although only performed in an extreme emergency, normally only when the woman is about to die. They are only about four months old and I am sure they are part of the reason you are in so much pain. You most certainly shouldn't be running with them or even moving around too much, but I can see you are determined to forget about the memories that happened on that day. They were so bad you didn't sleep for days afterwards and it scared you, but I can see you don't get scared easily, you're stronger than you let on, so it must've been bad. The scar on your stomach reminds you of it and you try your hardest to forget about the scars, the memories and move on." He concluded.

"You're perfectly right" Molly assured. A sad smile creeping onto her mouth as a single tear rolled down her face. Reaching down to her side Molly ripped the bullet out of her side, squinting in pain when doing so.

"What the hell did you do that for?" Anderson yelled and everyone looked at him. "To hurry everyone up, we all have things to do I'm sure."

With that John moved forward and started wiping alcohol gel onto the wound, before bringing the needle to the surface of her skin and sewing it shut. Within minutes the bullet wound was stitched up and Molly walked over to a wall panel which had a picture of angels painted onto it.

"What are you doing?" Sherlock questioned as Molly pulled out a keypad from behind a small table which sat next to the wall panel. "How did you know that was there?" John carried on asking, but she didn't reply and instead typed a ten number code into the keypad before pressing enter. Placing the keypad down on the table again, Molly bent down and placed her hand against the panel which lit up and scanned her hand for authorisation.

"Access granted using the highest authority, welcome M" The speaker next to the panel said as it slid back to reveal a deep hole in the wall which contained two guns, some black, fitted clothes and some other supplies. Picking up the clothes, Molly put them on and then placed one of the guns in her pocket, before turning back around to face the others.

"What the hell was that about?! Highest authority, welcome M! We thought you were dead also. I think I speak for everyone when I say we want answers!" John shouted.

From the corner of her eye, Molly could see a man in black near the window. Whipping her gun out, she turned to face him.

"What do you want?" Molly questioned as she cocked her gun at the man.

"Michael wants you to know he's calling off his people M. Meet him in the main hall in fifteen minutes, you are free to walk around the house as much as you want between now and then, no one is allowed to kill or shoot at you."

"Good considering this is my house!" Molly basically yelled. "I'll be there, but I have a few things to do first. Goodbye." She finished before pulling the gun's trigger and watching the man's body fall to the floor with a thud.

"Your house, Molly? You and Michael seem friendly" Sherlock stated.

"Oh do shut up Sherlock, you may be my equal but you don't know half the things I know, and you would never want to! Trust me." Molly whispered the last part.

Jonathan chose that point in time to walk through the doors. "Oh no" Where his first words, once looking at the people in the room. "I know" Molly replied. "You are now in triple the risk and your friends are in danger. In all fairness Boss, I would put security on Mr Holmes and co to make sure he doesn't get to them." He suggested.

"Yes, yes, what do you mean triple?"

"That's what I came to tell you. He's managed to block the helicopter openings; we couldn't fly the helicopter out of here. The kids aren't safe and the security is starting to fail, we need to get them out of here, but we can't take them out of the front doors, they would either be shot or kidnapped instantly."

Molly's face was completely pale by the time he finished.

"I'm sorry kids?" Sally asked.

Molly ignored her "What are the numbers like?"

"Twenty- two dead, all of them Michael's. Everyone on your team are alive still, but of course they would be, you only get the best."

"Ok I suggest, we head back to base, back up the security and meet him in the main hall in fifteen minutes. Oh and give every one clearance. I left my phone downstairs so I can't do it right now."

"Yes Boss" Patricks replied before moving out of the room, closely followed by Molly. "Are you lot coming? Or are you just going to stand there gaping at me the whole night?" Molly said sarcastically as the others started to follow her.

* * *

Molly and Patricks led the others into a dark room at the back of the house before locking the door. "Why did you lock the door? And actually answer me this time!" John questioned. "You'll see" Was Molly's only reply. The previously dark room lit up in a blaze of light which reached every corner of the small room.

"State your name and position" A voice echoed through the room.

"Molly, Molly M, the head of Consulting Spy organisations and Patricks, Jonathan Patricks, second hand man to Molly M" Molly called out.

"Welcome Boss, agent Patricks" The voice replied as the far wall slid up to reveal a staircase leading towards basement level.

* * *

**Thanks for reading. Not sure when the next chapter will be uploaded, but hopefully it won't take too long to write and upload.**


	5. Chapter 5

Molly, is that you?

Chapter 5

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**Hey Guys! Sorry it's been a while and it's a bit short, but oh well, here is Chapter 5.**

* * *

"Consulting Spy Organisations? What is this place? Molly please answer me this time" Greg pleaded as everyone made the short decent down the brightly lit stairs.

"I will explain in a minute as soon as we get into a secure room and I know my children are ok" Molly replied evenly, whilst taking a deep breath. "We're here" She finished pushing open the white door at the bottom of the stairs.

The room which led off from it was massive, computer screens covering every wall and desks lining the centre of the room, hundreds of people sat behind them.

"Welcome to the Consulting Spy Organisation's England headquarters." Molly told everyone, while they all gaped at the sight, everyone apart from Sherlock.

"Nice place you have here" He told her.

"Well I do try and this is only part of the headquarters. If you look to your right that door leads to the interrogation rooms and cells, the door to the left leads to the agents living quarters and if you follow me we can go to a meeting room and I will explain." Molly replied.

"Boss, before you go, we've targeted Hugo Gonzales in India, do you want to send a hit team over there?" a petite woman with blonde hair asked as she made her way over to the group.

"Yes, send the golem he's in that area. Oh and agent Williams, confirm dinner with him for two weeks' time, tell him to bring the wife and kids while you're at it." She replied before the woman walked away and Molly led the group into a large meeting room.

* * *

The meeting room was large and a long table took up most of the room. A woman holding a gun sat at one end with a baby in her arms and a little girl lay asleep to the left of her in one of the other chairs.

"Leave us Caroline, I can take it from here" Molly said to the woman as she walked over to the other woman and took the baby into her arms.

"Yes Boss" the woman replied before walking out of the room, closing the door behind her.

"Mummy?!" The little girl exclaimed waking up, she directed her attention towards Molly before looking towards Greg, Sally, John and Sherlock. "Are they? Mummy, what's happening? Why are my godparents here? I thought you said I would probably never see them." The girl said, her face masked from all emotions.

"Godparents?!" John asked.

"Yes about that John, you're all down as their godparents. Just in case anything happened to either me or my husband. Which you can agree something probably might considering our jobs. Oh and can you pass that bottle which is on the side over there to me please"

"Fine" John replied passing the bottle of milk to Molly, where she proceeded to wake the previously sleeping baby to give him his feed.

"So aren't you going to introduce us?" Sally asked looking down at the tiny baby in Molly's arms.

"Oh yes, this is Thomas and that sweetie over there is Ella" She replied gesturing to the little girl.

"Boss, we need to get a plan in place, your life and the children's are in a lot of danger, we only have another ten minutes before Michael and you are supposed to meet." Jonathan pointed out.

"Yes, yes, everyone sit down and I will explain the best I can."

* * *

"Way before I met you Sherlock, I set up the Consulting Spy Organisation, in fact when I was twelve. Since then it has grown. You could say it runs in the family, if you will."

"So you're telling me you lied to us the whole time we've known you?" Anderson pointed out.

"No, not really, you never asked."

"What does Michael Justicia want with you?" Greg asked this time.

Molly laughed at this "Revenge, a good time maybe, it's not my fault but I take it in my stride to protect those close to me. Like I did when Sherlock needed my help, I faked his death for him. I've kept as much trouble away from all your doors as possible, it may not seem like it but I never lied or pretended to be your friends, that was and is one hundred per cent real, but right now I need you to trust me for all our sakes."

"I think we can do that" John replied.

"Good, grab a gun each and follow me" Molly told them as they all walked back into the room filled with spies.

"Caroline, take them to the helicopter and I will override the security so you can take them out of here. Oh and remember same destination as before." Molly said to the woman as she passed Thomas to the woman and Ella let go of her mother's leg to take Caroline's hand. "Daddy will meet you there ok sweetheart." Molly addressed the girl this time. "And Agent Smith, do not under any circumstance let them out of your sight; you know how many people would do anything to get a hold of either of them."

"Yes Boss" The woman replied before walking away clutching both children.

"Ok people now to override the system I need to go to the devils lair, but don't worry I'll make sure they don't shoot you Sherlock" Molly said turning to them, with a smile.

"What do you mean the devils lair?" John asked.

"Let's just say my business empire doesn't just stop at spying." was Molly's only reply.

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**Until the next time my lovely readers - Lucy x**


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